RetrogeneDB ID: retro_cjac_3320

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:82862638..82862905(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000011474
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PDRG1
• Ensembl ID: ENSCJAG00000020766
• Aliases: None
• Description: p53 and DNA-damage regulated 1 [Source:HGNC Symbol;Acc:16119]

Sequence

>retro_cjac_3320
GAGGAGCTTGTTGAAGAAGTGCTGGTGAACAAGCAGCAGATTGTGGACGTGGACCCCAAAAGGAATCAAAACCCAGAGTG
CCTTAGAGCCCTGCAGAATGGTCTCAGCCTCTCTGAAGATGTGGTTTGCTTTGGGAACATGCTTATCAAGATGCCTCACC
CTCGGATGAAGGAAACGATTGAGAAAAATCGGGATCATCTGGATAAAGAAATAGAAATTATCTAAAAACAATGAGGCCCA
AGGCAAACCAGAGCCGAAGAATTTCAA

Alignment

ORF - retro_cjac_3320 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.33 %
• Parental protein coverage: 67.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EELAEEVLADKRQIVDLDTKRNQNREGLRALQKDLNPSEDVMVCFGSMFIKMPHPETKEMIEKDQDQLDK
          EEL.EEVL..K.QIVD.D.KRNQN.E.LRALQ..L..SEDV.VCFG.M.IKMPHP..KE.IEK..D.LDK
Retrocopy EELVEEVLVNKQQIVDVDPKRNQNPECLRALQNGLSLSEDV-VCFGNMLIKMPHPRMKETIEKNRDHLDK

Parental  EIEKLRKQLKVKVNRLFEAQ
          EIE...KQ......R..E.Q
Retrocopy EIEII*KQ*GPRQTRAEEFQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.02 RPM	4.66 RPM
SRP051959_heart	0.04 RPM	10.26 RPM
SRP051959_kidney	0.02 RPM	7.70 RPM
SRP051959_liver	0.00 RPM	6.04 RPM
SRP051959_lung	0.00 RPM	10.05 RPM
SRP051959_lymph_node	0.02 RPM	12.10 RPM
SRP051959_skeletal_muscle	0.00 RPM	11.62 RPM
SRP051959_spleen	0.00 RPM	12.27 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3320 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3320 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3320 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020766	1 retrocopy	retro_cjac_3320 ,
Homo sapiens	ENSG00000088356	1 retrocopy	retro_hsap_1037,
Gorilla gorilla	ENSGGOG00000024924	1 retrocopy	retro_ggor_818,
Macropus eugenii	ENSMEUG00000003915	1 retrocopy	retro_meug_1967,
Myotis lucifugus	ENSMLUG00000007377	1 retrocopy	retro_mluc_348,
Macaca mulatta	ENSMMUG00000000973	1 retrocopy	retro_mmul_824,
Nomascus leucogenys	ENSNLEG00000009712	1 retrocopy	retro_nleu_910,
Oryctolagus cuniculus	ENSOCUG00000016709	1 retrocopy	retro_ocun_1047,
Ochotona princeps	ENSOPRG00000006403	1 retrocopy	retro_opri_630,
Pongo abelii	ENSPPYG00000010897	1 retrocopy	retro_pabe_869,
Pan troglodytes	ENSPTRG00000013368	1 retrocopy	retro_ptro_707,